runTSNE: runTSNE

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Description

Wrapper for the Rtsne function. Users may call this directly or call it through the plotTSNE function and also pass additional arguments related to the Rtsne function.

Usage

runTSNE(object, ..., PCA, dims, seed, perplexity, theta)

## S4 method for signature 'EMSet'
runTSNE(object, ..., PCA = FALSE, dims = 2,
  seed = 0, perplexity = 30, theta = 0.5)

Arguments

object	An expression matrix or a PCA-reduced matrix.
...	Additional arguments to pass on to Rtsne function.
PCA	Set this PCA flag to TRUE if the object is a PCA-reduced matrix. Default: FALSE.
dims	Number of dimensions you would like to reduce to. Default: 2.
seed	(Optional) Set to a specific value for reproducible TSNE plots. Default: 0.
perplexity	(Optional) Numeric; perplexity parameter. Default: 30.
theta	(Optional) Numeric; Speed/accuracy trade-off. (increase for less accuracy). Default: 0.5.

Value

t-SNE coordinates in the "TSNE" slot of reducedDims

Examples

# Load example EMSet
em_set <- ascend::analyzed_set

# Run tSNE
em_set <- runTSNE(em_set, PCA = TRUE, dims = 2, seed = 1)

IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.